RetrogeneDB ID: retro_tbel_3231

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_134426:35068..35587(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: NDFIP2
• Ensembl ID: ENSTBEG00000005780
• Aliases: None
• Description: Nedd4 family interacting protein 2 [Source:HGNC Symbol;Acc:18537]

Sequence

>retro_tbel_3231
ACTGAAGTCTACAACGAGTTTTATCCTGTGCCACCTCCCTACAGTGCTGCTACCTCTCTTCCGACATACGATGAAGCTGA
GAAGGCTAAAGCTGCTGCAATGGCAGCTGCAGCAGCAGAAACGGCTCAAAGAATTCAGGAGGAAGAGTGTCCACCAAGAG
ATGATTTCAATGATGCACATCAACTTAGAGTGGGTAATGATGGCAATTTCATGCTGGCATTTTGCATGGCATTTATTTTC
AACTGGCTTGGATTTTGTTTATCCTTCTGTATCGCCAATACCATAGCTGGAAGGTACGGCGCTATCTGTGGATTGGGCCT
TTCATAGATCAAATGGATCCTTATTGTCAGGTTTTCTGATTATTTTACTGGATATTTTAATGGACAATACTGGCTTTGGT
GGATATTTCTTGTACTTGGACTACTACCTTTCTTCAGAGGATTTGTTAATTATCTAAAAGTCAGAAACATGTCTGAAAGT
ATGGCGGCCGCTCATAGAACAAGATATTTCTTCTTATTA

Alignment

ORF - retro_tbel_3231 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.38 %
• Parental protein coverage: 51.64 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TEVYNEFYPVPPPYSVATSLPTYDEAEKAKAAAMAAAAAETAQRIQEEECPPRDDFNDADQLRVGNDGIF
          TEVYNEFYPVPPPYS.ATSLPTYDEAEKAKAAAMAAAAAETAQRIQEEECPPRDDFNDA.QLRVGNDG.F
Retrocopy TEVYNEFYPVPPPYSAATSLPTYDEAEKAKAAAMAAAAAETAQRIQEEECPPRDDFNDAHQLRVGNDGNF

Parental  MLAFFMAFIFNWLGFCLSFCITNTIAGRYGAICGFGLSLIKWILIVRFSDYFTGYFNGQYWLWWIFLVLG
          MLAF.MAFIFNWLGFCLSFCI.NTIAGRYGAICG.GLS.IKWILIVRFSDYFTGYFNGQYWLWWIFLVLG
Retrocopy MLAFCMAFIFNWLGFCLSFCIANTIAGRYGAICGLGLS*IKWILIVRFSDYFTGYFNGQYWLWWIFLVLG

Parental  LLLFFRGFVNYLKVRNMSESMAAAHRTRYFFLL
          LL.FFRGFVNYLKVRNMSESMAAAHRTRYFFLL
Retrocopy LLPFFRGFVNYLKVRNMSESMAAAHRTRYFFLL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_3231 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3231 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021282	2 retrocopies	retro_cjac_2643, retro_cjac_2644,
Cavia porcellus	ENSCPOG00000014687	1 retrocopy	retro_cpor_753,
Loxodonta africana	ENSLAFG00000000864	1 retrocopy	retro_lafr_841,
Monodelphis domestica	ENSMODG00000001586	2 retrocopies	retro_mdom_1600, retro_mdom_48,
Mustela putorius furo	ENSMPUG00000003366	1 retrocopy	retro_mputfur_1079,
Tupaia belangeri	ENSTBEG00000005780	1 retrocopy	retro_tbel_3231 ,